The nuclear center at Yongbyon traces its roots back to 1965, when it received its first research reactor from the USSR. A generation of nuclear physics specialists in North Korea cut their teeth on this little reactor, and by 1974 they were able to fuel and operate it without Soviet help, using uranium mined within the country. In 1980, they were confident enough to begin construction on a five-megawatt reactor, which was finished and in operation by the end of 1987.

North Korea shut down its new reactor for three months in 1989, and unloaded spent fuel. While the government claims that they only removed a tiny bit (0.13 kg of plutonium), other estimates state that up to 15 kg of plutonium was taken out.

In that same year, U.S. military satellites picked up a new construction project at Yongbyon: a fifty-megawatt reactor, along with housing, testing facilities, and what appeared to be a third reactor rated at 200 megawatts. Defense analysts worked their calculators and projected that the two new reactors would give the North enough plutonium for fifty warheads a year. They were obviously for military purposes: no power lines connected them to the grid, and Donald Rumsfeld later remarked that hooking both of them up would blow out North Korea's power network entirely.

The construction went on unimpeded until 1992, when the International Atomic Energy Agency (IAEA) smelled a major rat. North Korea's official papers stated that only minor amounts of plutonium had been removed from the 5MW reactor (explained as "defective fuel rods"). Evidence on site, however, suggested that plutonium had been removed on several occasions. While the IAEA began pushing for more hard evidence, North Korea refused to allow them any further access to facilities, and in 1993, the country dropped out of the Non-Proliferation Treaty.

Over the next year, the United States began planning a surgical strike on Yongbyon, and the threat of war on the Korean peninusula became so intense that Billy Graham and Jimmy Carter went on emergency peace missions to meet Kim Il Sung. Carter managed to halt the slide into war by persuading Kim to meet with South Korean president Kim Young Sam, and even after the former Kim's death a month later, North Korea was willing to sign an Agreed Framework with the United States to shut down its operating reactor and cease construction on its two new reactors. In return for doing this, the US would supply them with two light water reactors, suitable for electricity but not for weapons.

The thaw in the wake of this agreement lasted until 2002. IAEA installed seals, cameras, and other equipment to monitor the Yongbyon reactor, which the North Korean authorities tolerated for all of eight years. Then, on December 21, 2002, the seals and cameras were removed at the reprocessing facility: Pyongyang claimed that the IAEA refused to respond to previous requests to deactivate the surveillance measures. Three days later, authorities began moving fuel back to the 5 MW reactor: the IAEA estimated that it would be operational by February 2003, and that warheads could be completed by June.

As of May, reprocessing facilities at Yongbyon do not appear to be operational. Some have speculated that the government may transport spent fuel rods to reprocessing centers elsewhere: others argue that Kim Jong Il is merely using the threat of restarting the nuclear program as a bargaining chip against the United States, South Korea, and Japan. This is how the Korean War continues today: at places like Yongbyon.